ICoorOrbitalData.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
//////////////////////////////////////////////////////////////////////
/// @begin AtomTypeSet
///
/// @brief
/// A class for reading in the orbital type properties
///
/// @detailed
/// This class contains the ORBITALS INTERNAL_ICOOR data that is read in from residue_io.cc. Actually,
/// the data is set when residue_io.cc calls the command from residuetype.cc set_orbital_icoor. The data
/// is set and chills out in memory until needed. The actual xyz coordinates are not stored at this point.
/// xyz coordinates are constructed when conformation/Residue.hh asks for the build function in this class.
/// At that point, the coordinates are built and returned.
///
/// But wait, you say, why do you store the names of the atoms instead of the index of the atoms!? Well, the
/// problem occurs when residuetype reorders the indices of the atoms. When this occurrs, the indices for the icoor
/// are not reordered here. Another problem ocurs because orbital indices are not reordered in this process because
/// orbital indices are seperate from the atom indices. Regardless, when you build the xyz coords, this step is transparent
/// because the function orbital_xyz() in residue.hh takes care of this conversion of indice to string.
///
/// @note NOTE!!!!!!!!!!! The internal coordinates cannot contain an orbital as the stub1, stub2, or stub3 atom.
/// This is because the xyz coordinates are not updated when the conformation changes. The stub1, stub2, stub2 atoms
/// must be actual atoms and not orbitals!!!!! (design feature or flaw? you decide)
///
///
/// @authors
/// Steven Combs
///
///
/// @last_modified December 12 2010
/////////////////////////////////////////////////////////////////////////

#ifndef INCLUDED_core_chemical_orbitals_ICoorOrbitalData_hh
#define INCLUDED_core_chemical_orbitals_ICoorOrbitalData_hh

// Project headers
// AUTO-REMOVED #include <core/chemical/ResidueType.fwd.hh>
// AUTO-REMOVED #include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.fwd.hh>
// AUTO-REMOVED #include <core/id/AtomID.hh>

// Utility headers
// AUTO-REMOVED #include <utility/exit.hh>

#include <core/types.hh>
#include <string>

//Auto Headers
namespace core{
namespace chemical{
namespace orbitals{

class ICoorOrbitalData{
public:

public:
  /// @brief default constructor
  ICoorOrbitalData();

  /// @brief construct ICoorAtomID by atom name and its ResidueType
  ICoorOrbitalData(
      Real phi,
      Real theta,
      Real distance,
      std::string stub1,
      std::string stub2,
      std::string stub3
  );

  ICoorOrbitalData(
    Real phi,
    Real theata,
    Real distance,
    Size stub1,
    Size stub2,
    Size stub3
  );




  Real phi() const;
  Real theta() const;
  Real distance() const;
  std::string stub1() const;
  std::string stub2() const;
  std::string stub3() const;

  Vector
  build(
      Vector stub1_xyz,
      Vector stub2_xyz,
      Vector stub3_xyz
  ) const;


  void replace_stub1(const core::Size atom1 )
  {
    s_stub1_=atom1;
  }

  void replace_stub2(const core::Size atom2)
  {
    s_stub2_=atom2;
  }
  void replace_stub3(const core::Size atom3)
  {
    s_stub3_=atom3;
  }

  core::Size get_stub1()
  {
    return s_stub1_;
  }
  core::Size get_stub2()
  {
    return s_stub2_;
  }
  core::Size get_stub3()
  {
    return s_stub3_;
  }


private:
  Real phi_;
  Real theta_;
  Real distance_;
  std::string stub1_;
  std::string stub2_;
  std::string stub3_;

  Size s_stub1_;
  Size s_stub2_;
  Size s_stub3_;



};




}
}
}


#endif /* ICOORORBITALID_HH_ */